ACEDB User Manual

Mary O'Callaghan, October 1993

Contents

Section 1: Getting Started

Glossary

Object
In ACEDB an "object" is an item, such as a sequence, a paper or an author, together with its attached data.
Class
We group together similar objects, such as loci or papers, within a "class". Loci and papers have a Locus and Paper class respectively.
Key
Each object is labelled with a "key". For instance, an object in the Author class might have the key "Smith J" and an object in the Multi_pt_data class might have the key "5149". Each key in a class is unique.
Tag
Each field within an object is labelled with a tag. For instance, Author objects have the tags Full_name, Address, Paper.

Using the Mouse

The right button is used to access menus.

The left button is usually used to choose a class, a key (an object is accessed through its key), or a button option. Picking once highlights a class or key, and implements a button option. Picking a class or key twice, or picking it once and pressing Return, respectively displays the class's keys or the key's object.

The middle button is only used to move around maps (see Sections 2 and 3).

When the word pick is used below it should be understood as meaning to pick the left mouse button twice, unless otherwise stated.

ACEDB Class Window

When ACEDB is started up, two windows appear. The first is the ACEDB class window. This window provides a listing of the various classes in ACEDB.

The ACEDB Class Window contains the following features:

"Template" Text Entry Box

This allows us to specify which of a class's keys we want listed in the Main Keyset Window (see "Keyset Windows" below), the second of the two windows displayed when ACEDB is started up.

The class whose keys are to be listed should be picked once in the ACEDB Class Window before the keys to be listed are specified in the Template box. When the keys have been specified either press return, or pick the class a second time, to get the listing.

An asterisk in the text entry box represents any characters e.g. to get a listing of all the unc loci, type unc* in the Template box.

The default setting for the Template box is an asterisk. Hence by default every key in the highlighted class is listed.

"Text Search" Text Entry Box

This is used to search all classes for a particular piece of text. A list of the keys whose objects contain the text is given in the Main Keyset Window.

Long Search

An entry in the Text Search Text Entry box is usually only searched for among short pieces of text in a class's objects. However, if the "Long Search" button is pressed long pieces of text, such as abstracts, are also searched. The search takes a bit longer than usual.

Process Box

This is the box to the right of the word "Classes" in the ACEDB Classes Window. This box indicates the state of a process. For instance, if a listing of authors is requested, the box will turn red while the request is being processed. Once the process is completed the box will revert to its usual green colour and contain the word "Ready".

Menu For ACEDB Class Window

Quit
quits ACEDB

Help
provides context-sensitive help

Clean Up
closes all windows other then this one

Program Status
provides information about the program

Add update file
used to add data files when starting up the system

Query
used to do complex queries - see section 6 for details

Query by Examples
provides a more user-friendly way to do complex queries, but dosen't contain all the query capabilities as yet.

Tablemaker
used to create data tables

DNA analysis
This is the same as the Analysis option in the Feature Map which will be explained in Section 5.
If you are a privileged user some extra items appear on the menu if you type "setenv ACEDB_SU" on the command line before starting ACEDB.

Add/Alias/Rename
This provides a window in which you create or delete an object (e.g. an author), change an object's key name, or give a key an alias.

Read Ace Files
When data needs to be added to the system, ace files are used. This option enables you to read in these files.

Align Maps
brings up a window that lets you remake the maps after new data has been entered

Read Models
to change database structure - beware!

Session Control
used to start/rename/destroy sessions

Dump
dumps out all the data in the system

Write Access
To change any data within the system you need write access.

Keyset Windows

A keyset is simply a set of keys. The second window which appears when you start up ACEDB is the "Main Keyset Window". This usually contains the list of keys requested in the "Template" text entry box of the ACEDB Class Window.

To see a key's object, such as a paper and its related data, pick the key. A window will now appear. This will contain a series of tags, such as Year and Volume, together with their data. When a piece of data is in boldface format, the data is itself a key for an object. If this key is picked, a window containing its object will be displayed.

If only one key is requested in the "Template" section of the ACEDB Class Window, the object of the single key in the keyset is usually automatically displayed.

When a locus, rearrangement, clone or sequence key is selected, however, its object's tags and data are not shown directly. Instead, keys for loci and rearrangements are displayed in the appropriate position on the genetic map and keys for clones and sequences are shown in the appropriate position on the physical map. In these cases, if the key on the map is picked, the key's object will appear. If you want to see a key's object without having to bring up a map first, choose the "Show all text" option on the keyset menu.

If a chromosome key is picked, the genetic map for that chromosome is displayed. The only way to see the chromosome's textual data is to use the "Show all text" menu option.

Other keysets can also be created. The number of keys in a keyset is listed at the the top left of the keyset. The user can move from one key to another using either the mouse or the arrow keys. He/She can also scroll through a large listing rapidly using the page up and page down button options.

When you pick the centre of the top of a keyset it becomes the "Selected Keyset" (Selected Keyset appears at the top of the window). The Selected Keyset has special significance for various keyset calculations. The calculations are implemented using the pull-down menu, activated when the window is picked once with the right mouse button.

Menu For Keyset Windows

Quit
closes this window

Help
provides context-sensitive help

Add keys
This is used to add or delete keys from this keyset.

Copy
creates a new keyset window with the same keys as the current keyset

Save
saves a keyset
AND
lists keys which are common to the current keyset and the Selected Keyset

OR
lists keys in the current keyset and/or the Selected Keyset

MINUS
lists keys in the current keyset less those in the Selected Keyset

XOR
lists keys which are in the current keyset or the Selected Keyset but not both

Ace Dump
dumps out the keys in the keyset together with their related tags and data

ASN Dump
Ignore

Name Dump
dumps out the keys listed in the keyset

Sequence Dump
This is used to load a sequence into a file. A sequence key should be highlighted before this option is selected.

Show as Text
This displays a key's object. It's useful for bypassing the map display usually given when a locus, rearrangement, sequence, chromosome, or clone is picked. The relevant key in the keyset should be highlighted before this option is selected.

Show Related Biblio
This shows the bibliography for a particular key's object. The relevant key should be highlighted before this option is selected.

Section 2: Genetic Map

The Genetic Map is used to display any genetically-mapped data, including loci, rearrangements, multi-point and 2-point-data, and balancers. A representation of the physical map is also included, as are cloned loci, even in cases where they have no genetic mapping data, to facilitate the intersection of the two maps.

Accessing the Genetic Map

Pick a chromosome in the ACEDB Class Window or a keyset window. Alternatively pick a locus or rearrangement and the area of the map containing it will appear.

Features of the Genetic Map Window (from left to right)

Locator and Marker Loci
The Locator is a vertical black line containing a green bar. The black line represents the whole chromosome and the green bar indicates which part of the chromosome can be seen to the right of the line. Some loci are marked on the Locator to give the user a rough idea where things are positioned on the chromosome.

Rearrangements
Single lines are deficiency rearrangements, double lines are duplication rearrangements. If you pick one, a window will appear with information about that rearrangement.

Contigs
The yellow bars show the Physical Map contig(s) for the chromosome being examined.

Loci without mapping data
The loci shown between the contigs and the scale are on the physical map but have not got genetic mapping data.

Scale
The units are centimorgans.

2_point_data and Multipoint data
This can only be seen when the GMap data button (see below) is used.

Loci
Those highlighted in yellow are cloned. If you pick a locus a window will appear with information about the locus.

Moving around the map

The zoom in/out buttons at the top of the page can be used to increase or decrease the amount of the chromosome shown.

The Locator can also be used to zoom in and out. In this case you pick the green bar with the middle mouse button and drag to the left or right to zoom in or out respectively. You can also use the Locator to move up and down the chromosome. In this case, pick the green bar with the left button and drag it up or down.

Picking with the middle mouse button anywhere to the right of the Locator produces a horizontal line which can be dragged up or down the scale. This is used to indicate the place on the scale where the data displayed should be centred. To scroll through screenfuls of the map rapidly, position the horizontal line at the top or bottom of the window and pick the line repeatedly.

Ways of accessing mapping data

Pick a locus and get the textual details about its rearrangement, 3-point and 2-point data.

To get a graphical representation of a locus's mapping data, highlight a locus and choose the GMap Data button option. Rearrangements which are now highlighted in green include the locus; those highlighted in blue do not. Any 3-point or 2-point-data relating to the locus is also shown. 3-point-data is represented as a vertical line with a small square box for each of the three loci. 2-point-data is the same except that there are 2 boxes.

Highlight a rearrangement and choose the GMap Data option. Loci which are then highlighted in green are covered by the rearrangement; those highlighted in blue are not.

Ways of getting to the Physical Map from the Genetic Map

Pick a locus which has yellow highlighting and then pick the clone within that locus.

Alternatively, pick the contig. This will show the Physical Map representation of what was being shown on the Genetic Map. The map will be centred at the position you picked. There are little markers on the contig which indicate the positions of the cloned loci on the contig.

Genetic Map Buttons

Columns
This produces a list of various types of objects which can be displayed on the genetic map, such as rearrangements and multi point data. Those with blue highlighting are displayed on the map. Pick an object to add or remove highlighting.

Whole
shows the current map in its entirety

Zoom In/Out
decreases/increases the map area displayed

Highlight
highlights any loci and rearrangements in the Selected Keyset

GMap Data
shows mapping data for the currently highlighted locus or rearrangement

Genetic Map Menu

Quit
closes the map

Help
provides context-sensitive help

Print Screen
prints what is currently shown in this window

Print Whole Map
prints the whole map

Preserve
When a new map is created, the current map will be preserved instead of being overwritten.

Recalculate
is used to recalculate the map when new map position data for loci or rearrangements is added.

Save Map
is used to save any changes made to the map

Hide Header
is used to get rid of the button options and the blue information bar at the top of the map.

Physical Chromosome Map

This feature shows the physically mapped objects of the chromosome. A vertical black line represents the chromosome. Contigs are shown by default, as yellow bars. The user can choose to have physically mapped h as cDNAs, and cloned loci, displayed. The objects users must import from a keyset (see "Physical Chromosions" below), are represented as small boxes.

You can move around the map in the same way you can move around the genetic map (see "Moving around the Map" above).

Physical Chromosome Map Buttons

Whole To bring up the entire chromosome
Zoom In/Out increases/decreases the amount of the map shown
Clear clears any data imported from a keyset

Physical Chromosome Menu options

Quit
closes the map

Help
provides context-sensitive help

Print
prints what is displayed in this window

Preserve
The current map will be preserved instead of being overwritten when a new map is created.

Recalculate
is used to recalculate the map when new physical map data is added.

Highlight Selectec Objects
highlights any units on the map which are in the Selected Keyset.

Add Selected Objects
imports and displays any physically-mapped units which are in the Selected Keyset
Subtract Selected Objects

removes any physically-mapped units in the Selected Keyset from the map.

Full Genome Distribution
This shows all the chromosomes.

Change Symbol Size
changes the size of the boxes representing physically-mapped units

Change Bump Sloppiness
changes the way boxes line up to the right

Section 3: Physical Map

Accessing the Physical Map

The Physical Map can be accessed via the Genetic Map (see section 2) or by picking a particular clone in the ACEDB Class Window or a keyset window.

Features of the Physical Map (from the bottom up)

Locator
This consists of a black line showing the backbone of the physical map and a green bar which indicates the part of the map displayed above. Cloned loci are marked on the black line as an extra guideline.

Text
These are remarks about the map and can be picked for further information.

Genetic Map bar
Pick this bar to go to the Genetic Map (the position is interpolated between the two nearest cloned loci). Loci are marked and can be picked for further text information.

Pairs of small vertical lines
These mark the position where cosmid "islands" are bridged by a YAC. They indicate that the length of the separation between the two islands is unknown.

Sequence Boxes
These yellow boxes represent areas which have been sequenced. If you highlight a sequence the related clone and cloned locus (if there is one) will also be highlighted. If you pick it a second time the Feature Map (ie the sequence analysis window) will appear.

Cosmids, cDNAs and YACs
Cosmids and YACs are represented by horizontal lines. cDNAs are simply positioned on the map. All clones can be picked for text information. Cosmids with asterisks have other cosmids buried underneath them. YACs represented by boldface horizontal lines are gridded, i.e. we have polytene filter information for them which can be probed with cDNAs etc.

Note: The arrow keys can be used to move from one clone, locus or remark to the next.

Moving around the map

The Locator can be used to zoom in and out. Pick the green bar with the middle mouse button and drag up or down to respectively increase or decrease the amount of the map displayed. The Locator can also be used to move left or right. Pick the green bar once with the left button and drag to the left or right.

Picking with the middle button anywhere above the Locator produces a vertical line which can be dragged left or right. This is used to indicate where the data displayed should be centred. You can scroll screenfuls to the left or right by picking repeatedly with the middle mouse button at the far left or right of the screen.

Physical Map Menu

Quit
closes this window

Help
provides context-sensitive help

Print
prints the contents of this window

Preserve
The current map will be preserved instead of being overwritten when a new map is created.

Redraw
Ignore

Recalculate
Used to recalculate the map when new physical map data is added.

Show all Remarks
This shows extra, less relevant, remarks. Select again to get rid of the remarks.

Show Selected Objects
restricts the clones on the map to those in the Selected Keyset

Highlight Selected Objects
highlights those clones on the map which are in the Selected KeySet

Unhighlight/Revert
removes highlighting from any loci or rearrangements on the map which are also in the Selected Keyset

Show All Buried Clones
shows all the clones that are "underneath" the canonical ones

To Genetic Map
If a locus or clone has been highlighted, this option will display the genetic map at the locus's or clone's estimated position.

Sequence
shows the sequence for the highlighted clone

Set Zoom
changes the size of the zoom

Set Display Depths
Here you can specify the number of lines used for each type of data. For instance, if you had a lot of YACs and very few cosmids you might choose to increase the number of lines for showing YACs.

Section 4: Clone_Grid Window

This display represents a high-density gridded filter. It can show hybridisation information for probes to a filter, and is used both to view data and enter it. In the worm ACEDB there is a filter POLY1 of representative YACs, and cDNA clones have been mapped via this to the physical map.

How to access the clone grid

The grid can be accessed by choosing the Clone_Grid option on the ACEDB Class Window menu.

What You See

You see a window with small boxes representing YACs. The YACs are laid out in the way they are organized on the filter.

If you highlight one of them you get the name of the yac in the Gridded Clone text entry box at the top of the window.

If you type the name of a yac in the Gridded Clone text entry box then the small box on the filter which corresponds to that yac will light up.

If you pick the Gridded Clone button itself you can then pick a yac in a keyset or the physical map menu and if it is on the filter it will be highlighted.

If you want to test where a cDNA hybridises to the grid, type the name of the cDNA in the Probe text entry box at the top left of the window.

If you pick the Probe button itself you can then pick a probe, such as a cDNA, on the physical map or a keyset, and if it hybridises to the filter the relevant small boxes will be highlighted.

There are two modes of action for double clicks on the boxes themselves:

Map Mode: if you double-click on a box you will see the corresponding location on the physical map. If the box was lit positive then any other positive neighbouring yacs will be combined in to define a single map location.

Edit Mode: when you click on a square you change the colour of the square. This lets you enter a hybridisation signal.

It is also possible to use pooled probes rather than single clone probes. This uses items in the Pool class (not used in worm ACEDB).

Menu for Clone Grid

Quit, Help, Print, Preserve
as normal

Centre <-> Surround
Lets you save the current pattern as a background for comparison with other hybridisation patterns.

Toggle name display
Shows full names of all clones in grid. Too big for screen but good for printing.

Toggle small display
Displays at life size for the filter, to allow overlaying of film during data entry.

Set small sizes
Sets the dimensions of the small display to allow accurate overlaying.

Display probe as tree
Like "Show as text" in keyset menu

Save data with probe
To store a hybridisation pattern with a probe (the one named in the probe box). Requires write access.

Set cluster range
Lets you set a value that determines how the map position is calculated for a probe that hits overlapping clones. If there is a gap bigger than this value then multiple map positions are registered.

Stats on keyset
Given that a keyset of probes is the selected keyset, this says how many map loci are defined by their hybridisation patterns, etc.

Change gridded clone
To edit the clone grid object (requires write access).

Section 5: Sequence Display

This is the most complex display window in the ACEDB package, with many options. To get to it select any sequence object, or a yellow bar in the physical map.

It resembles the genetic map window in general organisation. The direction of display is from top to bottom. Scrolling and zooming are achieved exactly as with the genetic map. In the main, information is only shown for the positive strand. The strand can be reversed and/or complemented using a pull-down menu from the "Reverse-Complement" button (press the right mouse button when the pointer is inside the button).

Many different types of information can be shown. Which are available at any one time are controlled by the Columns button.

Display Control

Columns
This button switches the screen to a menu screen that lets you pick which columns of information are displayed. Options are, in top to bottom order:

Locator
Bar representing whole sequence with green cursor showing current location

Clones
names and extents of cosmids sequenced

Up Genes
Splicing pattern of genes on the opposite strand, running bottom to top.

Restriction map
when you look for a "Motif" in the analysis window, the names of the matches are shown in the matching positions in this column

Summary bar
Yellow bar that is used to show locations of features

Scale
Shows coordinates with respect to current origin.

Down Genes
Splicing pattern of genes on the positive strand.

Temp_gene
The working gene when using genefinder.

Finished
different levels of hatching indicate different levels of completion of the genomic sequence. Not very useful because not currently kept up to date.

CDS Lines
show a horizontal line for each CDS = Coding Sequence = predicted gene. For use when zoomed right out, to see over all distribution.

CDS Boxes
like CDS lines, but a different shape symbol. Lines are better.

cDNAs
shows the cDNAs as small black boxes

Gene names
names of genetically defined genes that correspond to predicted sequences, in the correct vertical positions

Assembly Tags
data imported from the xbap sequence assembly database - under development

3 Frame Translation
as it says

ORF's
Shows stop codons in each frame as horizonal lines.

Coding Frame
For a predicted gene, shows the frame of each exon.

ATG
Shows all ATG's as small yellow boxes. After getting Genefinder features the width of the box varies according to the log probability of being an initiator methionine codon.

Coding Potential
Shows regions of high coding potential as grey boxes. The width depends on the likelihood of being coding.

Peptide Similarity
Rectangles show regions of BLASTX similarity to database proteins in the appropriate frame. The width varies according to score (significance).

Gene Translation
The translation of the currently selected gene. You must be selecting a gene, or an intron or exon for this to work.

DNA Similarity
Regions of BLASTN similarity to DNA sequences.

Inverted Repeats
as it says

Tandem Repeats
as it says

User Segments
a facility for reading in a file of features from an outside program, defined by a sequence name, start and end positions in the sequence and a score. These are drawn as yellow rectangles, with the width depending on score.

Splices
Used to show Genefinder predictions of splice sites. 3' and 5' sites are differentiated by directional hooks. Length is proportional to log significance level.

Coords
Coordinates for the DNA.

DNA Sequence
The DNA sequence itself. Whenever any other feature is picked the corresponding DNA region is highlighted.

Brief_Identifications
gives a short description (a word or two) for the type of proteins that a predicted gene matches

Text Features
Any text attached to the sequence, including EMBL annotation etc.

Other control features

The Origin data entry box at the top of the window allows you to reset the origin by typing in a relative position. Also, if you click on the Origin button you can then click on any feature in the window, and its startpoint will become the new origin (e.g. a predicted gene, or an exon).

The "Active zone" is the region in which various analytical tools will operate, such as searches for restriction sites. It is also the region that will be written out as a sequence file by the "Export Sequence" menu option. You can change it by typing new values into the text entry box at top right (don't forget to hit return). The bounds of the active zone are shown by blue lines adjacent to the yellow summary bar.

There is a light blue reporting row below the active zone box and above the buttons that shows information about the currently selected object.

The Genefinder submenu operates like the Reverse-Complement submenu described above, and gives access to the Genefinder prediction package of Phil Green. The details of this package are beyond this manual.

The Clear button removes any highlighting and clears the summary bar.

Sequence menu

Quit, Help, Print Screen/Whole Map, Preserve
as normal

Recalculate
This is used to recalculate the map when new data has been added.

Clear DNA
Equivalent to the Clear button.

EMBL dump
Only for the C. elegans sequencing project (unfortunately).

Hide header
Hides the header for pretty printouts.

Color exons
If a gene is selected and the DNA is being displayed then this highlights all the exons and introns in the DNA sequence in alternating green and yellow.

Export translation
If a gene is selected this appends the translation of the gene to a file in FASTA format.

Export translations
dumps to a file the translations of all predicted coding sequences in the current active zone

Export Sequence
Writes out the DNA sequence for the current active zone to a user defined file.

Statistics
Prints out a summary of all features for the current sequence to the standard output.

Read User Segments
read in the data to be displayed in the "User segments" column (see Columns above)

Analysis window
Starts the DNA analysis package in a new window.

DNA Analysis Window

This is either accessed from the last entry of the sequence display menu, or from the "DNA" entry of the ACEDB Class Window menu. It provides various forms of simple DNA sequence analysis, either applied to a single sequence in the current sequence display window, or to whole sets of sequences defined by a keyset. This choice of single sequence or keyset is controlled by the toggle button at top. There is another toggle on the right between DNA and AA (amino acids). Many features only work for DNA.

The text entry line (yellow) allows you to type a simple search pattern (using IUPAC nucleotide codes) or the name of a restriction enzyme (from the Restriction class downloaded from Rebase -- Rich Roberts). You can in fact type several patterns, separated by semicolons. The cutpoints will be shown below in the analysis window, and if you are working with a single sequence the sites will be highlighted on the summary bar and in the displayed sequence.

Other functions are accessed by buttons, as below:

Finger print
Restricts with the enzymes used for the worm physical map HindIII and Sau3aI. The sites are shown in 2 colours in the feature window.

Motif Key_Set
Will import a list of motifs that can then be searched for in the active sequence or keyset of sequences.

Max mismatch
If this is not zero, it allows an approximate match of the sequence to the motif (restriction site). The value is the number of allowed mismatches. e.g. attgcc matches atagcc if "Max mismatch" is set to 1 (or more).

Dump Sequence
If UseKeySet is set, dumps in fasta format all sequences of the active keyset (the Selected Keyset). Else, dumps in fasta format the active region of the active sequence window, e.g. you can fasta dumps bases 3800 to 7000 of a given sequence.

EMBL dump
This dumps any EMBL data for the active sequence or keyset of sequences into a file.

Splice Concensus
Gives the 5' and 3' splice concensus sequences around the introns exons boundaries in the sequences of the active keyset. The result is shown in the analysis window itself. Resize the window to see it.

Codon Usage
Gives the codon usage in the sequences of the active keyset. The result is shown in a new window. Note that the genetic code is accessible via the online help package.

Sequence Lengths
Gives the histogram of the lengths of the individual sequences in the active KeySet.

Show gels
Pops a Gel Tool with its own help page.

Clear
Clears the Dnacpt window, useful before using Splice concensus or restrict buttons.

Section 6: Query Window

There are currently two query options in the main ACEDB window menu. One, "Query by example" is very user_friendly but has not got the full range of capabilities at present. The second "Query" is slightly less user friendly but has all the query capabilities. This section deals with Query but I have included a small section on Query by Example at the end.

General Comments

Queries are used to list keys and their data with particular conditions attached.

Conditions are stated on command lines which are activated when picked. If the bottom command line is edited a new empty one will appear. You can combine various commands by joining them with semi-colons; the result of each command is passed into the next one. Typing new commands on each line and activating them separately will give the same result (if the same keyset is used throughout).

If we specify a class on the command line all members of that class will be examined for the stated conditions relating to them and their tags. If we specify a tag without giving a class then all the class members currently in the selected keyset will be examined.

Output is directed to the Selected Keyset.

Syntax

If you want a class searched put either of the following: "Find Classname" or ">?Classname". A tag, such as the Paper tag within the Author class, should be simply stated as "Tagname" if you want a list of all the class keys which have something in that tag. However if you want the actual data for a key's tags you should say ">Tagname". See examples one and two below.

The conditions given should become progressively more specific. For instance, you might put a class first, then the conditions pertaining to the name of keys in that class, then a tag within that class, and lastly the conditions pertaining to the tag.

The following operators can be used in queries. In order of precedence:

  |  OR         in either (union)
  ^  XOR        in one or the other but not both
  &  AND        in both (intersection)
  !  NOT
  
Some tags have subfields to their right in a key window. The NEXT command is used to access these (see Example 8 below).

The HERE command is used for multiple checks on the one spot (see Example 9 below).

The COUNT command counts what is to the right. See example 5 below.

Parentheses such as "(" or "[" can be used but must be matched.

The conditions given for tags or classes must have double quotes if the text includes any of the following: & | ^ < > = ( ) [ ] { }

EXAMPLES

 1
    >?Author                  (or FIND Author)
In this case a class is given without any qualifying conditions, so each member of the class will be listed.

 2  (a) 

            Paper
No class has been specified, only a tag within a class. Hence keys of any class (within the Selected Keyset) are examined, but only those containing a paper will be listed.

    (b)  
            >Paper            (or FOLLOW Paper)
This is similar to 2(a) but in this case rather than showing the items that contain papers, we show the papers they contain.

 3
       >?Author s*|a*
In this case it's specified that only members of the author class whose name begins with s or a should be listed

 4
       >?Paper Journal=Nat* AND Year > 1987
Here, in addition to specifying the class Paper, we're giving conditions for data in the tags Journal and Year within the Paper class's keys. The papers of interest are those in journals beginning with Nat and whose year of publication is later than 1987.
 5
       >?Locus myo* Clone
In this case we're interested in the Locus class keys whose title begins with myo* and whose the locus class keys contain clones. As indicated before, if a tag, such as Clone, is stated without any conditions attached then all members of the class which have something in this tag are included.
 6
       >?Author IS "Sulston JE"; >Paper; >Author
Here we have a combination of commands. The result of each command feeds into the next. The aim is to get the authors who collaborated on papers with John Sulston. The three commands are as follows: The first gives the key Sulston JE. The second command gives all the papers for the key resulting from the first command, so we get all the papers by Sulston JE. The third command gets all the authors for the keys resulting from the second stage, so we get all the authors for papers by Sulston JE .
 7
      >?Author COUNT Paper > 10
This will list all authors who have more than 10 papers recorded in ACEDB.
 8  
      >?Locus gMap = X AND NEXT > 12 
NEXT is used to locate a subfield to the right of a tag. In this case we're looking for keys in the Locus class which contain X in the gMap (i.e. chromosome name) tag. Also the gMap tag's subfield, namely the Position field immediately to its right, which we get by using the command NEXT, should contain a position which is greater than 12.
 9
      >?Locus gMap = X AND NEXT > 12 AND HERE < 19
This is similar to Example 8 except for the last part. The command HERE lets us give a second condition to the field currently being examined (in this case the Position subfield). Hence, only keys whose gMap Position subfield is both greater than 12 and less than 19 will be listed.

Query Menu

Quit
Quits this window with an option to save your current set of commands

Help
provides context-sensitive help

Print
prints this window

Clear entries
clears the current instructions on the command lines

New Keyset
opens a new keyset window

Query by Example
see below

Load from File
loads a previous set of instructions from a file

Save to File
saves the current set of commands to a file

Search Locally
Implements the search

Send
Ignore

Undo
cancels the last command and redisplays the previous keyset

The button options are the same as the menu options.

Query by Example

Query by Example, as stated earlier, is very user friendly but hasn't got the full range of query capabilities. The following is a brief description of how it can be used.

First indicate what you want the search done on, a whole class of objects or a keyset of objects, by toggling the button with the word "From:" to its right.

Then indicate the class to which the objects should belong, by selecting an item to the right of the word "Class:". The selection can be made by toggling through the classes, or by picking the Class: button with the right mouse button and choosing from the resulting list of classes. Tags and data fields for that class will appear below.

Then it is necessary to indicate any limitations you want to place on the objects to be listed. If you are only interested, for instance, in finding Papers which have an entry in their Abstract tag, pick the Abstract tag. If you want to look at papers which have a particular kind of entry in a particular tag then you must type the condition in the green box to the right of the relevant tag. For instance, if you were only interested in Papers which have an entry beginning with Nat in the Journal tag, type Nat* in the green box to the right of the Journal tag.

Lastly, pick the "Search Locally" button to see the result.